Various assays have been developed to detect HIV. A common HIV-1detection assay utilizes quantitative polymerase chain reaction (PCR) as a means to amplify and detect viral RNA present in patient plasma. HIV-1positive individuals undergoing combination antiviral therapy (i.e., receiving two or more anti-HIV-1compounds) can exhibit decreased viral loads in the peripheral blood. In some cases, after several weeks or months of therapy, HIV-1RNA cannot be detected in the peripheral blood, indicating possible eradication of HIV-1in those individuals. Unfortunately, if patients exhibiting such a seemingly negative result stop therapy in the face of continued viral replication below the sensitivity of detection assays, the HIV can rebound very rapidly. Thus, the limited sensitivity of HIV detection assays provides a challenge to further advances in therapy.
Highly active antiretroviral therapy (HAART) with reverse transcriptase and protease inhibitors markedly suppresses HIV replication in the majority of infected patients. However, in a significant percentage of patients, viruses acquire mutations in their reverse transcriptase and protease genes that confer decreased sensitivity to the reverse transcriptase and protease inhibitors. This leads to drug failure, a resumption of viral replication, and a negative impact on patient survival. To combat drug resistance, clinicians switch therapies to drug combinations not previously administered to the patient. However, drug resistance mutations can confer resistance to a broad spectrum of reverse transcriptase and protease inhibitors. More effective clinical management of patients is achieved if the drug-resistance mutations are identified early so that treatments can be adjusted to those that are effective against the particular strain (e.g., mutant) of HIV. In view of this, viral genotyping is becoming an established procedure for monitoring of patients on HAART and has a significant impact on patient survival.
Viruses bearing drug-resistance mutations cannot generally be identified unless they comprise a significant percentage of a patient's viral population. As a consequence, the drug-resistant viruses are usually identified relatively late in the process leading to drug failure. Therefore, there is an urgent need for approaches that provide early identification of drug-resistance viral variants in patients.